We knew going into this months issue of Batman: Knight of Vengeance that Thomas Wayne was Batman, and that a mugger had apparently killed his wife and son, instead of him and his wife.
But at the tail end of issue, Jim Gordon had gone into Wayne Manor in search of The Joker and Harvey Dents twin children, whom had been kidnapped. Jim actually kills one of the children, who had been made up to appear as the Joker about to execute the other one. As he goes to check on the girl, Joker slits his throat.
Thomas Wayne shows up and his screams reveal that he’s known the Joker’s identity all along.
Martha Wayne.
Though if you read Flashpoint first this week, you may have noticed a clue there. While Barry is telling Thomas about remembering his son, we are shown the Wayne burial plots out back, and while there are a few in the distance, only one is front and center. The name hard to make out, which I’d imagine was to fuel rumors that Joker would actually be Bruce.